QuarterbackSteve Young had his best NFL season and won his second MVP award. Steve Young set what was, at the time, the NFL record for highest passer rating in a season – 112.8.[3]Cold Hard Football Facts states that Young's 1994 season is the second greatest passing season in NFL history.[4]

For the third consecutive season, the 49ers met the Cowboys in the NFC Championship Game. From the mid-1980s to the mid-1990s, the AFC was widely regarded as the NFL's inferior conference. Thus, this meeting between the NFC's perennial powerhouses was dubbed by many as "the real Super Bowl." The contest was one of the highest rated non-Super Bowl games in NFL history.

The 49ers would go on to defeat the Chargers in Super Bowl XXIX. Young was named the game's MVP with a record six touchdown passes.

In 1994, after the retirements and departures of several stalwarts from the late 80's and early 90's teams, the 49ers spent large amounts of money on the addition of several star free agent veterans. The revamp focused mainly on defense, where six new starters including Ken Norton, Jr., Gary Plummer, Rickey Jackson, and Deion Sanders were implemented, all with the ultimate goal in mind of dethroning the Dallas Cowboys. Said safety Merton Hanks, "Those players came in on one and two-year deals and they understood, 'if we do not get it done this year this organization is going to blow itself up.'" Additionally, several rookie players made key contributions to the team, some becoming season-long starters. This included defensive tackle Bryant Young, fullback William Floyd, and linebacker Lee Woodall. The 49ers started slowly early in the season. They defeated the Raiders in a game where Jerry Rice broke the NFL record for touchdowns, but followed with a 24–17 loss to the Kansas City Chiefs, led by former 49ers quarterback Joe Montana.

Despite victories over the Rams and Saints, the 49ers offensive line was struggling having lost four starters to injury, and in Week 5 the Niners were crushed 40–8 by the Eagles. Following the Eagles game, a poll conducted on local sports radio station KNBR showed that an overwhelming majority of 49er fans wanted head coach George Seifert fired.

The game against the Eagles was a turning point for the 49ers despite being a lopsided loss. Steve Young was benched for Elvis Grbac abruptly during a series in the 3rd quarter. Soon after, Young was livid on the sidelines, shouting profanities at head coach George Seifert. Young later admitted "I was looking for a fistfight", and would later say that this incident caused his teammates to respond better to his leadership, as they saw how much he cared about winning ("It galvanized the guys behind Steve", said Brent Jones).

The following week in Detroit, the 49ers trailed the Lions 14–0. After throwing a pass, Young was hit, picked up, and driven into the ground by three Lions defenders. After the hit, Young was screaming with his face dark red in color. He crawled most of the way off of the field before refusing help from the trainers as he limped the remaining way off the field. He miraculously returned to the field one play later (NFL rules state that after trainers attend to an injured player, that player must leave the field for at least one play – Elvis Grbac came in for that one play and threw an incompletion) to lead the 49ers to a 27–21 victory.

The team rallied around Young to win 10 straight games, including a 21–14 victory over the two-time defending Super Bowl champion Cowboys. During that span, the 49ers' average margin of victory was nearly 20 points per game; they broke 35 points scored seven times, four times breaking 40 points scored.

During the 1994 season, many NFL teams wore "throwback uniforms" for occasional games (after week 2 of the season) to celebrate the NFL's 75th anniversary (a corresponding diamond 75th Anniversary patch was also worn by all teams). The 49ers chose to wear a version of their 1955 uniforms as throwbacks. This design featured sans-serif block numerals that were outlined and shadowed in black. White pants with thinner red-black-red striping were also worn, along with the old striped red socks (the team later reverted to their regular solid red socks after receiving permission from the NFL to wear the uniforms starting from Week 10 until Super Bowl XXIX). The team's regular 1989–95 gold helmet was worn with this uniform, as there was no logo on the 1955 helmet.

The team first donned the 1955 throwback uniforms during a week 3 match against the Los Angeles Rams and the following week at home versus the Saints. Both games ended in victory (coincidentally, these were also the first two games Deion Sanders played with the 49ers after signing as a free-agent after week 2). The team then suffered an embarrassing 40–8 loss to the Philadelphia Eagles at home wearing their regular red uniforms with gold pants. (Football statistics site Football Outsiders calculates this 49ers loss to be the second-most lopsided football game they'd tracked from 1994–2008.)

For the subsequent three games until their BYE week, the team again was scheduled to play games wearing the throwback uniforms with white pants and blockshadow numerals, and all three games resulted in wins. During the following weeks the 49ers embarked on a 10-game winning streak. The team, prompted both by the superstition of coach George Seifert, and the preference of players, petitioned the NFL to wear the throwback uniforms for the rest of the season. The league granted the request and the switch to solid red socks after the BYE week marked this occurrence. In all, the team went 15–1 (including the playoffs) wearing the 1955/1994 throwback uniforms. The only loss occurred during the regular season finale at Minnesota, with the team wearing white jerseys and resting most of their starters for the playoffs. Meanwhile, the 49ers went undefeated wearing the red jerseys of the throwback uniform. After winning Super Bowl XXIX however, the team was compelled to revert to wearing its regular 1964-style uniforms (1991 revised design) for the following 1995 season. One year later, the throwback design strongly influenced the 49ers to redesign their uniform set. In 1996, the team revealed a new helmet and uniform design featuring a darker red, shadowed numbers, black accents, and white pants. In 1998, the team changed the pants to a gold color and wore these uniforms through the 2008 season. The 49ers brought back the 1994 white throwback uniform design as an alternate set for the 2018 season.

This was the much-hyped match between Joe Montana and Steve Young. Montana threw two touchdowns and a two-point conversion while Young had a touchdown and two interceptions and was sacked for a safety; the Niners also fumbled twice. San Francisco sports bars airing the game saw viewers overwhelmingly cheer for Montana's Chiefs over Young and the Niners.

Steve Young was benched after going 11 of 23 with two interceptions and getting sacked for a safety by William Fuller; Elvis Grbac completed four of eight passes and was sacked twice. The Eagles outgained the Niners in yardage 437 to 189.

The Lions jumped to a 14-0 lead on a Brett Perriman touchdown catch and a nine-yard score from Barry Sanders. Young was knocked out for one play with a pinched nerve in his leg; he came back in despite heavy pain and rallied the Niners to 27 unanswered points.

Ex-Falcon Deion Sanders returned to the Georgia Dome and ran back a 93-yard interception for a touchdown. Steve Young threw four touchdowns while Jeff George threw four interceptions; it was the second six-turnover game for the Falcons that season.

The 49ers posted their first win over the Cowboys since 1990. The game was tied 7-7 until the Niners scored in the final three minutes of the third quarter on a 57-yard Jerry Rice touchdown catch. Following an exchange of four consecutive punts Troy Aikman was intercepted by Merton Hanks; the ensuing Niners drive took fifteen plays and ended on a Brent Jones touchdown catch just before the two-minute warning. A very late Cowboys touchdown was followed by an unsuccessful onside kick and Niners win.

In their last home meeting with the Rams as a Los Angeles team until 2016, the Niners blew a 21-6 lead and trailed 27-24; Jerry Rice fumbled with 6:05 to go but the Rams had to punt. Steve Young threw on seven of the next ten plays and connected with Rice for the go-ahead score with 1:56 to go; the Rams failed on 4th and 20 and the Niners were winners.

After a Brent Jones fumble on their first drive of the game, in which the Bears converted with a field goal by Kevin Butler, the 49ers went on to score 37 unanswered points to rout the Bears 44-15, including scoring 23 in the second quarter. The Bears would not score until the fourth quarter when the game was already out of reach. An endzone brawl erupted late in the second quarter following Steve Young's six-yard rushing score. Shaun Gayle of the Bears pushed Young to the dirt after the score; when Young threw the ball in the ground and in Gayle's face a fight erupted.

The 49ers were looking to make a statement after being knocked out of the playoffs the previous 2 years by the Cowboys. The 49ers, thanks to 3 consecutive turnovers by the Cowboys to start the game, broke out to a 21-0 lead in the 1st quarter. It started with an interception by Eric Davis that was returned 44 yards for a touchdown just on the third play of the game, a Michael Irvin fumble that set up a 29-yard screen pass by Steve Young to Ricky Watters for a touchdown, and then a fumble on the ensuing kickoff in which the 49ers converted with a one-yard touchdown run by William Floyd. The 49ers went into halftime up 31-14 after a 28-yard pass by Young to Jerry Rice. The Cowboys fought back in the 2nd half, but fell short and the 49ers won 38-28, advancing to their 5th Super Bowl. The Cowboys turned the ball over 5 times, which ended up being a major factor in the game. The 49ers also handed Troy Aikman his first ever loss as a starting quarterback in the post season.

(*)The Chargers became the first team to have a successful two-point conversion in the Super Bowl. This was the first season in which the NFL allowed 2-point conversions (a rule in place in the American Football League in San Diego's first ten seasons), and the Chargers actually had two in the game.